Israeli military sources said the target was a cemetery near Bait Hanoun, a Gaza town near the border with Israel.
The missiles were fired after helicopters spotted some Palestinian fighters who were getting ready to fire Qassam rockets into Israeli territory, the sources said.
Two bodies recovered from the scene were too badly damaged to be immediately identified, Palestinian witnesses and medics said.
Palestinian residents said they thought the missiles had hit an empty field near Israel. They also heard machine-gun fire from the helicopters but they had no immediate reports of casualties.
Earlier, residents initially said the target was a metal foundry.
Israeli helicopters target metal workshops in the occupied Gaza and the West Bank regularly. They allege the foundries are used to produce munitions and rockets that are fired by Palestinian fighters into illegal Jewish settlements.